MolNFT v1 · #135313 · protein
Crystal structure of achbp from aplysia californica complex with 2- aminopyrimidine at pH 8.0 spacegroup P21
5TVH · Soluble acetylcholine receptor: “Crystal structure of achbp from aplysia californica complex with 2- aminopyrimidine at pH 8.0 spacegroup P21”. X-ray diffraction, 2 ligands (7KO, NAG), 20 pockets (best druggability 0.71). MolNFT v1…
- PDB
- 5TVH
- Type
- protein
- Length
- 1,064 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble acetylcholine receptor
- UniProt
- Q8WSF8
- Ligands
- 7KO, NAG
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Soluble acetylcholine receptor | protein | 214 | 13% helix, 48% strand | Q8WSF8 |
| B | Soluble acetylcholine receptor | protein | 209 | 10% helix, 47% strand | Q8WSF8 |
| C | Soluble acetylcholine receptor | protein | 211 | 13% helix, 46% strand | Q8WSF8 |
| D | Soluble acetylcholine receptor | protein | 217 | 12% helix, 47% strand | Q8WSF8 |
| E | Soluble acetylcholine receptor | protein | 213 | 13% helix, 45% strand | Q8WSF8 |
Ligands and binding sites
- 7KO · 6-chloro-N~4~,N~4~-bis[(pyridin-3-yl)methyl]pyrimidine-2,4-diamine · ligand · 5 copies · chains A, E, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains D
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.71 | 0.81 | 56 | 7KO |
| 2 | 581 | 0.71 | 0.80 | 61 | 7KO |
| 3 | 445 | 0.70 | 0.81 | 57 | 7KO |
| 4 | 538 | 0.66 | 0.77 | 52 | 7KO |
| 5 | 503 | 0.66 | 0.77 | 39 | 7KO |
Interfaces
5 interfaces between chains.
- A–E · 1382 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1365 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1339 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1300 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1279 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5TVH · Crystal structure of AChBP from Aplysia californica complex with 2-aminopyrimidine at pH… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q8WSF8
- Elsewhere: RCSB PDB 5TVH · PDBe 5TVH · UniProt Q8WSF8
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